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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $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' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ), 'gf_id' => 'HOM05D001151', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001151' ), 'data_identifier' => 'HOM05D001151', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001151', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '537', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28460' => 'bna', 'A03p49200' => 'bna', 'A03p49220' => 'bna', 'A05p41640' => 'bna', 'A06p47100' => 'bna', 'A08p11830' => 'bna', 'A08p14840' => 'bna', 'Aa31LG5G16910' => 'aar', 'Aa31LG6G2780' => 'aar', 'Aa31LG9G1810' => 'aar', 'Aa31LG9G1840' => 'aar', 'Aa31LG9G8660' => 'aar', 'Actinidia00049' => 'ach', 'Actinidia11300' => 'ach', 'Actinidia14319' => 'ach', 'Actinidia23425' => 'ach', 'Actinidia27480' => 'ach', 'Actinidia40227' => 'ach', 'Actinidia40229' => 'ach', 'Actinidia40230' => 'ach', 'Ah.08g209870' => 'amhyb', 'Ah.13g074530' => 'amhyb', 'AL3G17340' => 'aly', 'AL7G33500' => 'aly', 'AL7G39800' => 'aly', 'AL7G39810' => 'aly', 'AL7G39830' => 'aly', 'AL7G39840' => 'aly', 'AL8G15270' => 'aly', 'AL962U10010' => 'aly', 'Aqoxy2G03101' => 'aox', 'Aqoxy4G00085' => 'aox', 'Aqoxy5G00609' => 'aox', 'arahy.Tifrunner.gnm1.ann1.091D1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BVQ2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.664S68' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80N87M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.881TBE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8C0M2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W9XSW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GVD99J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RH6BR7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S6J9QN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WJ8WCF' => 'arhy', 'AT3G06390' => 'ath', 'AT4G15610' => 'ath', 'AT4G15620' => 'ath', 'AT4G15630' => 'ath', 'AT4G20390' => 'ath', 'AT5G44550' => 'ath', 'ATR0706G093' => 'atr', 'ATR0706G150' => 'atr', 'ATR1098G060' => 'atr', 'Atru.chr10.657' => 'acertr', 'Atru.chr4.2759' => 'acertr', 'Atru.chr4.2760' => 'acertr', 'Atru.chr4.2764' => 'acertr', 'Atru.chr5.1264' => 'acertr', 'AUR62006324' => 'cqu', 'AUR62026363' => 'cqu', 'AUR62030119' => 'cqu', 'AUR62030120' => 'cqu', 'AUR62041204' => 'cqu', 'AUR62042518' => 'cqu', 'BcaB03g11671' => 'bca', 'BcaB04g18302' => 'bca', 'BcaB07g30519' => 'bca', 'BcaC01g00668' => 'bca', 'BcaC03g16673' => 'bca', 'BcaC05g29813' => 'bca', 'BcaC05g30031' => 'bca', 'BcaC06g31607' => 'bca', 'BcaC06g32947' => 'bca', 'BcaC06g32948' => 'bca', 'BcaC06g32949' => 'bca', 'BcaC06g33419' => 'bca', 'BcaC06g33421' => 'bca', 'BcaC06g34540' => 'bca', 'BcaC07g37893' => 'bca', 'BolC2t10546H' => 'bol', 'BolC3t20574H' => 'bol', 'BolC5t34742H' => 'bol', 'BolC7t43272H' => 'bol', 'BolC7t45248H' => 'bol', 'BolC8t48289H' => 'bol', 'BraA02t07881Z' => 'bra', 'BraA03t14019Z' => 'bra', 'BraA03t14022Z' => 'bra', 'BraA05t22883Z' => 'bra', 'BraA06t27582Z' => 'bra', 'BraA08t33172Z' => 'bra', 'BraA08t33468Z' => 'bra', 'C02p45080' => 'bna', 'C03p82910' => 'bna', 'C05p60850' => 'bna', 'C07p27420' => 'bna', 'C07p47250' => 'bna', 'CANSAT35G0921' => 'cansat', 'CANSAT78G1018' => 'cansat', 'CANSAT78G1682' => 'cansat', 'CANSAT78G1982' => 'cansat', 'CARHR080920' => 'chi', 'CARHR178560' => 'chi', 'CARHR227220' => 'chi', 'CARHR290010' => 'chi', 'CARHR290030' => 'chi', 'Carub.0003s0583' => 'cru', 'Carub.0007s2077' => 'cru', 'Carub.0007s2617' => 'cru', 'Carub.0007s2618' => 'cru', 'Carub.0007s2620' => 'cru', 'Carub.0008s0395' => 'cru', 'Ca_02383_v3' => 'car', 'Ca_09116_v3' => 'car', 'Ca_21547_v3' => 'car', 'Ca_21548_v3' => 'car', 'Cc03_g02280' => 'ccan', 'Cc03_g02290' => 'ccan', 'Cc09_g07160' => 'ccan', 'CDE02G4221' => 'cde', 'Cfa000752' => 'cfa', 'Cfa006022' => 'cfa', 'Cfa015348' => 'cfa', 'Cfa015349' => 'cfa', 'Ciclev10005986m.g' => 'ccl', 'Ciclev10005989m.g' => 'ccl', 'Ciclev10006657m.g' => 'ccl', 'Ciclev10006955m.g' => 'ccl', 'Ciclev10016765m.g' => 'ccl', 'Ciclev10023477m.g' => 'ccl', 'CiPaw.01G152500' => 'cil', 'CiPaw.01G152600' => 'cil', 'CiPaw.02G086100' => 'cil', 'CiPaw.02G086200' => 'cil', 'CiPaw.07G101000' => 'cil', 'CiPaw.09G149300' => 'cil', 'ClCG00G005340' => 'cla', 'ClCG01G008950' => 'cla', 'ClCG05G005810' => 'cla', 'ClCG05G005820' => 'cla', 'ClCG05G005830' => 'cla', 'ClCG09G006410' => 'cla', 'COL.COLO4_13923' => 'col', 'COL.COLO4_26866' => 'col', 'Cpa.g.sc16.115' => 'cpa', 'Cpa.g.sc16.116' => 'cpa', 'Cpa.g.sc832.1' => 'cpa', 'CsaV3_1G046760' => 'csa', 'CsaV3_3G014160' => 'csa', 'CsaV3_3G014170' => 'csa', 'CsaV3_3G014180' => 'csa', 'CsaV3_6G017410' => 'csa', 'CsaV3_7G028730' => 'csa', 'CSS0011260' => 'camsi', 'CSS0014959' => 'camsi', 'CSS0017094' => 'camsi', 'CSS0028548' => 'camsi', 'CSS0048143' => 'camsi', 'DCAR_002445' => 'dca', 'DCAR_002446' => 'dca', 'DCAR_002448' => 'dca', 'DCAR_005843' => 'dca', 'DCAR_007799' => 'dca', 'DCAR_024545' => 'dca', 'DCAR_024546' => 'dca', 'DCAR_024547' => 'dca', 'DCAR_024548' => 'dca', 'DCAR_024605' => 'dca', 'DCAR_024610' => 'dca', 'DCAR_027106' => 'dca', 'Dinv11973' => 'din', 'Dinv38320' => 'din', 'Dinv38321' => 'din', 'Dinv44422' => 'din', 'Duzib052G1206' => 'dzi', 'Duzib138G0426' => 'dzi', 'Duzib151G0042' => 'dzi', 'Duzib151G0589' => 'dzi', 'Duzib212G0419' => 'dzi', 'Duzib212G0620' => 'dzi', 'Duzib235G0035' => 'dzi', 'ECA233G3000' => 'eca', 'ECA240G1210' => 'eca', 'ECA240G1769' => 'eca', 'ECA240G4474' => 'eca', 'ECA248G2052' => 'eca', 'EL10Ac3g06570' => 'bvu', 'EL10Ac3g06571' => 'bvu', 'EL10Ac3g06737' => 'bvu', 'EL10Ac4g08227' => 'bvu', 'EL10Ac4g08352' => 'bvu', 'EL10Ac7g17030' => 'bvu', 'Eucgr.A00513' => 'egr', 'Eucgr.B01267' => 'egr', 'Eucgr.H01205' => 'egr', 'Eucgr.H03772' => 'egr', 'FAN07G2269' => 'fan', 'FAN12G0210' => 'fan', 'FAN12G1597' => 'fan', 'FAN12G3527' => 'fan', 'FAN17G0704' => 'fan', 'FAN22G1580' => 'fan', 'FAN25G0432' => 'fan', 'FvH4_3g11410' => 'fve', 'FvH4_4g17250' => 'fve', 'FvH4_4g17260' => 'fve', 'FvH4_4g17290' => 'fve', 'Glyma.03G209700' => 'gma', 'Glyma.07G251200' => 'gma', 'Glyma.07G251300' => 'gma', 'Glyma.08G129300' => 'gma', 'Glyma.09G083400' => 'gma', 'Glyma.13G215500' => 'gma', 'Glyma.15G097400' => 'gma', 'Glyma.15G097600' => 'gma', 'Glyma.15G191800' => 'gma', 'Glyma.17G023000' => 'gma', 'Glyma.17G023100' => 'gma', 'Glyma.19G207000' => 'gma', 'Glyma.U031308' => 'gma', 'Gohir.A02G046400' => 'ghi', 'Gohir.A02G046500' => 'ghi', 'Gohir.A06G119400' => 'ghi', 'Gohir.A09G233500' => 'ghi', 'Gohir.A10G101220' => 'ghi', 'Gohir.A11G117300' => 'ghi', 'Gohir.D02G052100' => 'ghi', 'Gohir.D02G052200' => 'ghi', 'Gohir.D06G123800' => 'ghi', 'Gohir.D09G234600' => 'ghi', 'Gohir.D10G167000' => 'ghi', 'Gorai.005G057400' => 'gra', 'Gorai.005G057500' => 'gra', 'Gorai.006G257500' => 'gra', 'Gorai.007G131100' => 'gra', 'Gorai.010G144000' => 'gra', 'Gorai.011G186300' => 'gra', 'GSVIVG01010992001' => 'vvi', 'GSVIVG01017795001' => 'vvi', 'GSVIVG01017796001' => 'vvi', 'GSVIVG01037957001' => 'vvi', 'HanXRQChr01g0002001' => 'han', 'HanXRQChr03g0080151' => 'han', 'HanXRQChr03g0080161' => 'han', 'HanXRQChr03g0080171' => 'han', 'HanXRQChr03g0080181' => 'han', 'HanXRQChr06g0173931' => 'han', 'HanXRQChr11g0342561' => 'han', 'HanXRQChr11g0342571' => 'han', 'HanXRQChr12g0366261' => 'han', 'HanXRQChr13g0387581' => 'han', 'HanXRQChr13g0388541' => 'han', 'HanXRQChr13g0410881' => 'han', 'HanXRQChr13g0410891' => 'han', 'HanXRQChr15g0465211' => 'han', 'Haze_01258' => 'cav', 'Haze_01259' => 'cav', 'Haze_01260' => 'cav', 'Haze_01261' => 'cav', 'Haze_04828' => 'cav', 'Haze_05971' => 'cav', 'Hma1.2p1_0078F.1_g040790' => 'hma', 'Hma1.2p1_0761F.1_g214360' => 'hma', 'Hma1.2p1_0823F.1_g224680' => 'hma', 'Hma1.2p1_1028F.1_g249560' => 'hma', 'Hma1.2p1_1485F.1_g286490' => 'hma', 'Hma1.2p1_1485F.1_g286500' => 'hma', 'HPP92_010733' => 'vpl', 'HPP92_011825' => 'vpl', 'HPP92_013695' => 'vpl', 'HPP92_013696' => 'vpl', 'HPP92_016867' => 'vpl', 'HPP92_016877' => 'vpl', 'HPP92_016917' => 'vpl', 'HPP92_016921' => 'vpl', 'HPP92_017179' => 'vpl', 'HPP92_017673' => 'vpl', 'HPP92_018398' => 'vpl', 'Hund20579' => 'sun', 'Hund21556' => 'sun', 'Hund28066' => 'sun', 'Hund28075' => 'sun', 'Lalb_Chr07g0177571' => 'lal', 'Lalb_Chr08g0233151' => 'lal', 'Lalb_Chr13g0303851' => 'lal', 'Lalb_Chr13g0303861' => 'lal', 'Lalb_Chr18g0047441' => 'lal', 'Lj1C37G11' => 'lonja', 'Lj1C37T13' => 'lonja', 'Lj1g0005041' => 'lja', 'Lj2A338T75' => 'lonja', 'Lj3C812G7' => 'lonja', 'Lj4g0003966' => 'lja', 'Lj4g0006946' => 'lja', 'Lj4g0007248' => 'lja', 'Lj6A670G70' => 'lonja', 'Lj6A670T85' => 'lonja', 'Lj6g0010921' => 'lja', 'LjContig00389g0013761' => 'lja', 'Lsat_1_v5_gn_1_111521' => 'lsa', 'Lsat_1_v5_gn_3_24880' => 'lsa', 'Lsat_1_v5_gn_5_50001' => 'lsa', 'Lsat_1_v5_gn_5_50121' => 'lsa', 'Lsat_1_v5_gn_5_50161' => 'lsa', 'Lsat_1_v5_gn_5_50201' => 'lsa', 'Lsat_1_v5_gn_5_50820' => 'lsa', 'Lsat_1_v5_gn_5_51020' => 'lsa', 'Lsat_1_v5_gn_5_51120' => 'lsa', 'Lsat_1_v5_gn_6_16401' => 'lsa', 'Manes.03G069600' => 'mes', 'Manes.03G191500' => 'mes', 'Manes.15G016300' => 'mes', 'Manes.15G016400' => 'mes', 'Mapoly0004s0021' => 'mpo', 'Mapoly0049s0096' => 'mpo', 'Mapoly0159s0027' => 'mpo', 'MBI02_g45109_MAGBIO' => 'mbi', 'MBI18_g22376_MAGBIO' => 'mbi', 'MBI18_g28206_MAGBIO' => 'mbi', 'MBI18_g31498_MAGBIO' => 'mbi', 'MBI19_g30847_MAGBIO' => 'mbi', 'MD05G1263600' => 'mdo', 'MD10G1241300' => 'mdo', 'MD13G1173100' => 'mdo', 'MD13G1173400' => 'mdo', 'MD13G1173500' => 'mdo', 'MD16G1174700' => 'mdo', 'Medtr0097s0070' => 'mtr', 'Medtr2g020060' => 'mtr', 'Medtr4g118800' => 'mtr', 'Medtr4g118810' => 'mtr', 'Medtr7g108130' => 'mtr', 'Medtr8g089300' => 'mtr', 'MELO3C006608.2' => 'cme', 'MELO3C006609.2' => 'cme', 'MELO3C006610.2' => 'cme', 'MELO3C015901.2' => 'cme', 'MELO3C021356.2' => 'cme', 'MELO3C021781.2' => 'cme', 'Migut.G00204' => 'egut', 'Migut.G00205' => 'egut', 'Migut.M01934' => 'egut', 'Migut.N00119' => 'egut', 'MSTRG.10058' => 'ama', 'MSTRG.10059' => 'ama', 'MSTRG.10060' => 'ama', 'MSTRG.16311' => 'ama', 'MSTRG.21812' => 'ama', 'MSTRG.24778' => 'ama', 'MSTRG.24779' => 'ama', 'MSTRG.3949' => 'ama', 'MSTRG.3950' => 'ama', 'Nitab4.5_0000824g0050' => 'nta', 'Nitab4.5_0000829g0040' => 'nta', 'Nitab4.5_0000829g0070' => 'nta', 'Nitab4.5_0002719g0040' => 'nta', 'Nitab4.5_0002986g0050' => 'nta', 'Nitab4.5_0002986g0090' => 'nta', 'Nitab4.5_0006863g0010' => 'nta', 'Nitab4.5_0009550g0020' => 'nta', 'Nn3g21309' => 'nnu', 'Nn3g21310' => 'nnu', 'Nn3g21312' => 'nnu', 'Nn4g26011' => 'nnu', 'Nn4g26012' => 'nnu', 'Nn7g37742' => 'nnu', 'Oeu021625.1' => 'oeu', 'Oeu021626.1' => 'oeu', 'Oeu026200.1' => 'oeu', 'Oeu044784.1' => 'oeu', 'Oeu052707.1' => 'oeu', 'Oeu060327.1' => 'oeu', 'Oeu062890.2' => 'oeu', 'Oeu062891.1' => 'oeu', 'Os01g0363300' => 'osa', 'Os07g0442900' => 'osa', 'Os12g0610800' => 'osa', 'Peaxi162Scf00067g01120' => 'pax', 'Peaxi162Scf00386g00921' => 'pax', 'Peaxi162Scf00386g00931' => 'pax', 'Peaxi162Scf00670g00341' => 'pax', 'PGR004G2765' => 'pgr', 'PGR031G2659' => 'pgr', 'PGR083G0430' => 'pgr', 'PGR119G1471' => 'pgr', 'PGSC0003DMG400011355' => 'stu', 'PGSC0003DMG400021195' => 'stu', 'PGSC0003DMG400022659' => 'stu', 'PGSC0003DMG400022677' => 'stu', 'Phvul.001G202900' => 'pvu', 'Phvul.003G101100' => 'pvu', 'Phvul.003G101200' => 'pvu', 'Phvul.006G161700' => 'pvu', 'Phvul.006G161900' => 'pvu', 'Phvul.009G218200' => 'pvu', 'Potri.001G442300' => 'ptr', 'Potri.008G205000' => 'ptr', 'Potri.008G205100' => 'ptr', 'Potri.011G154900' => 'ptr', 'Prupe.1G141500' => 'ppe', 'Prupe.1G141600' => 'ppe', 'Prupe.1G141700' => 'ppe', 'Prupe.4G101900' => 'ppe', 'Psat1g019520' => 'psa', 'Psat1g187320' => 'psa', 'Psat3g024400' => 'psa', 'Psat4g030520' => 'psa', 'Psat4g030560' => 'psa', 'Psat7g060880' => 'psa', 'PSO017G4965' => 'pso', 'PSO170G1278' => 'pso', 'PSO170G2703' => 'pso', 'PSO170G6376' => 'pso', 'PSO210G1907' => 'pso', 'PSO210G3892' => 'pso', 'PSO210G6211' => 'pso', 'PSO478G5177' => 'pso', 'PSO541G3810' => 'pso', 'PSO541G5365' => 'pso', 'PSO675G2175' => 'pso', 'PSO675G8581' => 'pso', 'PSO675G9129' => 'pso', 'PSO782G2220' => 'pso', 'PSO832G3482' => 'pso', 'QL05p063075' => 'qlo', 'QL06p007522' => 'qlo', 'QL06p007531' => 'qlo', 'QL06p007556' => 'qlo', 'QL12p024282' => 'qlo', 'RcHm_v2.0_Chr4g0421171' => 'rch', 'RcHm_v2.0_Chr4g0421181' => 'rch', 'RcHm_v2.0_Chr4g0421251' => 'rch', 'RcHm_v2.0_Chr5g0018351' => 'rch', 'Rhsim02G0013000' => 'rsi', 'Rhsim02G0013100' => 'rsi', 'Rhsim02G0013200' => 'rsi', 'Rhsim02G0013300' => 'rsi', 'Rhsim02G0167800' => 'rsi', 'Rhsim04G0216700' => 'rsi', 'Rhsim04G0216800' => 'rsi', 'Sabra08G0156900' => 'sbr', 'Sabra08G0157000' => 'sbr', 'Sabra11G0144800' => 'sbr', 'Sabra16G0298900' => 'sbr', 'Sabra16G0300800' => 'sbr', 'SalBow2G0349' => 'sbo', 'SalBow2G2129' => 'sbo', 'SalBow5G0713' => 'sbo', 'SalBow5G4849' => 'sbo', 'SalBow8G0157' => 'sbo', 'SalBow8G1344' => 'sbo', 'Sc05g0002950' => 'sci', 'Sc05g0003220' => 'sci', 'Sc13g0003590' => 'sci', 'Sc15g0003710' => 'sci', 'Sc19g0004960' => 'sci', 'Sed0001505' => 'sed', 'Sed0007070' => 'sed', 'Sed0016845' => 'sed', 'Sed0020890' => 'sed', 'Sed0027287' => 'sed', 'SEGI_09363' => 'sgi', 'SEGI_31363' => 'sgi', 'SEGI_34631' => 'sgi', 'SGA_v2.0_scaffold175G39319' => 'sas', 'SGA_v2.0_scaffold223G42882' => 'sas', 'SGA_v2.0_scaffold57G20237' => 'sas', 'SGA_v2.0_scaffold86G26832' => 'sas', 'SGA_v2.0_scaffold86G26838' => 'sas', 'SHI00298' => 'shi', 'Solyc01g067300.3' => 'sly', 'Solyc01g067330.3' => 'sly', 'Solyc02g069730.3' => 'sly', 'Solyc09g074550.3' => 'sly', 'Sopen01g029100' => 'spe', 'Sopen01g029210' => 'spe', 'Sopen02g018850' => 'spe', 'Sopen09g029380' => 'spe', 'Sp3g05310' => 'spa', 'Sp7g13880' => 'spa', 'Sp7g18760' => 'spa', 'SpUn0297_0010' => 'spa', 'SpUn0446_0010' => 'spa', 'SpUn0524_0010' => 'spa', 'TAR362G0497' => 'tar', 'TAR362G1028' => 'tar', 'TAR365G0728' => 'tar', 'TAR627G1052' => 'tar', 'THA.LOC104802560' => 'tha', 'THA.LOC104818843' => 'tha', 'THA.LOC104820241' => 'tha', 'THA.LOC104820243' => 'tha', 'Thecc.01G292000' => 'tca', 'Thecc.04G278200' => 'tca', 'Thecc.04G278300' => 'tca', 'Thecc.06G005200' => 'tca', 'Thhalv10001033m.g' => 'esa', 'Thhalv10021548m.g' => 'esa', 'Thhalv10026298m.g' => 'esa', 'Thhalv10026308m.g' => 'esa', 'Thhalv10026349m.g' => 'esa', 'TPR.G14964' => 'tpr', 'TPR.G1538' => 'tpr', 'TPR.G27588' => 'tpr', 'TPR.G28534' => 'tpr', 'TPR.G32286' => 'tpr', 'TPR.G6272' => 'tpr', 'TWI09G1149' => 'twi', 'TWI09G1306' => 'twi', 'TWI09G1310' => 'twi', 'TWI14G0495' => 'twi', 'TWI38G0934' => 'twi', 'TWI53G0843' => 'twi', 'TWI63G0399' => 'twi', 'unitig_22.g6335' => 'ugi', 'unitig_32.g10785' => 'ugi', 'unitig_32.g11751' => 'ugi', 'unitig_8.g2880' => 'ugi', 'unitig_8.g3085' => 'ugi', 'vmacro02502' => 'vma', 'vmacro08198' => 'vma', 'vmacro08199' => 'vma', 'vmacro10996' => 'vma', 'vmacro15255' => 'vma', 'vmacro22598' => 'vma', 'VMungo0251G2869' => 'vmu', 'VMungo0540G1263' => 'vmu', 'VMungo0540G2050' => 'vmu', 'VMungo1215G0580' => 'vmu', 'VMungo1215G2032' => 'vmu', 'VMungo1309G2278' => 'vmu', 'VMungo1309G2621' => 'vmu', 'VMungo1383G1588' => 'vmu', 'Zm00001eb031580' => 'zma', 'Zm00001eb094710' => 'zma', 'Zm00001eb131630' => 'zma', 'Zm00001eb305660' => 'zma' ) $gf_id = 'HOM05D001151' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001151' ) $data_identifier = 'HOM05D001151' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 6, 'bra' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 5, 'dca' => (int) 12, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 6, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 14, 'cav' => (int) 6, 'hma' => (int) 6, 'vpl' => (int) 11, 'sun' => (int) 4, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 6, 'lsa' => (int) 10, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 9, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 6, 'ptr' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 15, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 7, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 5, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 8, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb305660' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1